Villanueva is also the founder of the Philippines for Jesus Movement (PJM), which has more than forty bishops from different Christian churches nationwide as members.

He was immersed in both student and labor movements in the 1970s, joining the progressive segments of society which opposed Marcos' dictatorship.

During Martial law, he fought local landgrabbers in Bulacan and ended up being jailed twice for his political beliefs and participation in various mass actions.

In 2007, JIL stated it had "over five million members today in 18 cities in Metro Manila, 80 provinces in the Philippines and 60 countries in the world.

"[11][12] Villanueva is against same-sex marriage; he said in an interview, "According to the Bible, don't imitate what happened in Sodom and Gomorrah because judgment will befall on the country if it's done".

Despite the polls done by Social Weather Stations and Pulse Asia showing him trailing among the four contenders,[14] Villanueva was confident that he would win the elections saying that "this is why we do not believe in the surveys of the two companies that are usually commissioned by political parties here — because the more than three million human bodies (at my rally) can indicate the real results of the survey.

[8][17] He married Dr. Adoracion "Dory" Villanueva (née Jose) on June 5, 1971, and their marriage lasted until her death on March 10, 2020.

Jonjon was charged with murder for allegedly ordering the shooting of a soldier of the Armed Forces of the Philippines during the May 2007 elections.

[8] Their daughter, Joni Villanueva-Tugna, was a Christian singer, TV host, and Mayor of Bocaue from July 2016 until her death on May 28, 2020.